Flooding in Devon before Christmas. More floods may be on the way in south-west England and south Wales. Photograph: Ben Birchall/PA

The Environment Agency is warning that "significant disruption" could be possible from flooding in the south-west of England and south Wales as heavy rain and strong winds batter parts of the UK.

Rescuers searching for a missing fisherman off the coast of Devon found a body, and in Scotland it emerged that a marine scientist died apparently after being hit by lightning.

Met Office amber severe weather warnings were in place for Devon and Cornwall, where there was a threat of up to 50mm of rain falling on moors and hills. There were also amber warnings for parts of Scotland, with winds as high as 85mph predicted on exposed spots.

Yellow warnings, one down from amber, were issued for the rest of the south-west of England, most of Wales and the remaining parts of Scotland.

The Environment Agency urged communities in south-west England and south-east Wales to prepare for further flooding on Tuesday and into Wednesday. A spokesman said: "High ground in Wales, Dartmoor and Exmoor is most likely to be affected, and strong winds could lead to some disruption along the coast as waves and spray come over the top of defences."

Almost 50 properties in England and Wales have flooded since Saturday. About 50 flood warnings are in place, meaning flooding is expected, along with almost 200 alerts, meaning flooding is possible. The agency said the numbers were expected to grow.

The spokesman said: "Larger rivers including the Lower Exe [in Devon] and the Severn will continue to rise throughout the week. Environment Agency teams are deploying mobile flood barriers at Ironbridge, Bewdley and Shrewsbury to protect communities from flooding from the river Severn."

Off the Devon coast rescuers called off a search for a missing six-metre fishing boat after an RNLI lifeboat found a body. The boat, named JCK, was last seen at 6.25pm on Monday off Torquay and had been due back at Brixham harbour at 7pm, but the boat and its skipper did not arrive.

A Brixham coastguard spokesman said: "Debris of the JCK has also been found at various points off the coastline. It is believed that the body is that of the fisherman on board the JCK. The search has been called off. Because of the gale-force weather, we think the rest of the vessel will be blown ashore by itself."

The man is understood to have been a local operating regularly out of south Devon.

In Port Appin, Argyll, western Scotland, the body of a scientist, Tim Boyd, was found by a dog walker on a bridge near his home. Police are investigating the theory that he may have been struck by lightning. A large storm in the area at the time of his death on Sunday afternoon knocked down power and phone lines.

A Strathclyde police spokeswoman said: "Police were called to a report of the sudden death of a 54-year-old man in Port Appin, Argyll, around 1.25pm on Sunday. There would appear to be no suspicious circumstances; however, a postmortem will be carried out in due course to establish the exact cause of death. A full report will be sent to the procurator fiscal."

Boyd worked at the Scottish Association of Marine Science (Sams) in Oban. A spokesman said: "We are grief-stricken about the tragic death of Tim Boyd, who was killed by a lightning strike on Sunday afternoon. Our hearts go out in particular to his wife and his two talented daughters he was so very, very proud of. Our thoughts are with his family."

Boyd joined Sams in 2007 from Oregon State University in the US and was well respected internationally for his expertise in Arctic oceanography.